Though the chancel is of the 13thc., the W tower and four-bay nave arcade of the 14thc.; the clerestory is later, done in the perpendicular style. The N chapel is probably from the 17thc. Restoration by William White in 1868. In the W tower there are some reset Romanesque voussoirs.

In the late 11thc. Heydour was a jurisdiction of nearby Osbournby. Domesday records both a priest and a church here in 1086. By the early 12thc. St. Michael's was part of the endowment of the Dean and Chapter at Lincoln cathedral.

Gaping chevron voussoirs are very rare in the county. Though these at Heydour may have once formed part of an arch, it is clear from the misalignment of the individual voussoirs that they are reset in this wall.